A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes.

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.

Overcoming the Failure of Correlation for Out-of-Plane Motions in a Simple Aromatic: Rovibrational Quantum Chemical Analysis of c-C3H2.

Truncated, correlated, wave function methods either produce imaginary frequencies (in the extreme case) or nonphysically low frequencies in out-of-plane motions for carbon and adjacent atoms when the carbon atoms engage in π bonding. Cyclopropenylidene is viewed as the simplest aromatic hydrocarbon, and the present as well as previous theoretical studies have shown that this simple molecule exhibits this behavior in the two out-of-plane bends (OPBs). This nonphysical behavior has been treated by removing nearly linear dependent basis functions according to eigenvalues of the overlap matrix, by employing basis sets where the spd space saturatation is balanced with higher angular momentum functions, by including basis set superposition/incompleteness error (BSSE/BSIE) corrections, or by combining standard correlation methods with explicitly correlated methods to produce hybrid potential surfaces. However, this work supports the recently described hypothesis that the OPB problem is both a method and a basis set effect. The correlated wave function's largest higher-order substitution term comes from a π → π* excitation where constructive interference of both orbitals artificially stabilizes the OPB. By employing schema to overcome this issue, the symmetric OPB ν9 is the predicted to be the second-brightest transition, and it will be observed very close to 775 cm-1. However, more work from the community is required to formulate better how carbon atoms interact with their adjacent atoms in π-bonded systems. Such bonds are ubiquitous in all of chemistry and beyond.

Communication: The failure of correlation to describe carbon=carbon bonding in out-of-plane bends.

Carbon-carbon multiply bonded systems are improperly described with standard, wave function-based correlation methods and Gaussian one-particle basis sets implying that thermochemical, spectroscopic, and potential energy surface computations are consistently erroneous. For computations of vibrational modes, the out-of-plane bends can be reported as imaginary at worst or simply too low at best. Utilizing the simplest of aromatic structures (cyclopropenylidene) and various levels of theory, this work diagnoses this known behavior as a combined one-particle and n-particle basis set effect for the first time. In essence, standard carbon basis sets do not describe equally well sp, sp2, and sp3 hybridized orbitals, and this effect is exacerbated post-Hartree-Fock by correlation methods. The latter allow for occupation of the π and π* orbitals in the expanded wave function that combine with the hydrogen s orbitals. As a result, the improperly described space is non-physically stabilized by post-Hartree-Fock correlation. This represents a fundamental problem in wavefunction theory for describing carbon.

Escherichia coli dihydrofolate reductase catalyzed proton and hydride transfers: temporal order and the roles of Asp27 and Tyr100.

The reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) has become a model for understanding enzyme catalysis, and yet several details of its mechanism are still unresolved. Specifically, the mechanism of the chemical step, the hydride transfer reaction, is not fully resolved. We found, unexpectedly, the presence of two reactive ternary complexes [enzyme:NADPH:7,8-dihydrofolate (E:NADPH:DHF)] separated by one ionization event. Furthermore, multiple kinetic isotope effect (KIE) studies revealed a stepwise mechanism in which protonation of the DHF precedes the hydride transfer from the nicotinamide cofactor (NADPH) for both reactive ternary complexes of the WT enzyme. This mechanism was supported by the pH- and temperature-independent intrinsic KIEs for the C-H→C hydride transfer between NADPH and the preprotonated DHF. Moreover, we showed that active site residues D27 and Y100 play a synergistic role in facilitating both the proton transfer and subsequent hydride transfer steps. Although D27 appears to have a greater effect on the overall rate of conversion of DHF to tetrahydrofolate, Y100 plays an important electrostatic role in modulating the pKa of the N5 of DHF to enable the preprotonation of DHF by an active site water molecule.

Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase.

Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and (13)C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor-acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for significant electrostatic changes in the active site microenvironments due to conformational motion occurring over the catalytic cycle of ecDHFR.

Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding.

The vibrational Stark effect provides insight into the roles of hydrogen bonding, electrostatics, and conformational motions in enzyme catalysis. In a recent application of this approach to the enzyme ketosteroid isomerase (KSI), thiocyanate probes were introduced in site-specific positions throughout the active site. This paper implements a quantum mechanical/molecular mechanical (QM/MM) approach for calculating the vibrational shifts of nitrile (CN) probes in proteins. This methodology is shown to reproduce the experimentally measured vibrational shifts upon binding of the intermediate analogue equilinen to KSI for two different nitrile probe positions. Analysis of the molecular dynamics simulations provides atomistic insight into the roles that key residues play in determining the electrostatic environment and hydrogen-bonding interactions experienced by the nitrile probe. For the M116C-CN probe, equilinen binding reorients an active-site water molecule that is directly hydrogen-bonded to the nitrile probe, resulting in a more linear C≡N--H angle and increasing the CN frequency upon binding. For the F86C-CN probe, equilinen binding orients the Asp103 residue, decreasing the hydrogen-bonding distance between the Asp103 backbone and the nitrile probe and slightly increasing the CN frequency. This QM/MM methodology is applicable to a wide range of biological systems and has the potential to assist in the elucidation of the fundamental principles underlying enzyme catalysis.

Molecular simulations of the structure and dynamics of water confined between alkanethiol self-assembled monolayer plates.

We have studied structural and dynamic properties of water confined between hydrophobic alkanethiol self-assembled monolayers (SAMs) using molecular-dynamics simulations. After quantifying the hydrophobic nature of the SAM surfaces via contact-angle calculations involving water droplets, we analyze the effect that the hydrophobic surfaces have on structural properties of the confined water such as density, tetrahedral ordering, orientational structure at the SAM-water interface, and on dynamical properties via calculation of diffusion coefficients. Both the SPC/E and TIP5P water models have been utilized in the calculations. All of the analyses of the structure and dynamics of water are performed as a function of separation from the surface with a focus on determining the range of the effect of hydrophobic surfaces on the water film. We show that the effects of the surface are not noticeable at water-film depths of approximately 1 nm for the structural properties examined. However, calculated diffusion coefficients in the plane of the surface indicate the SAMs induce enhancement of water motion clearly beyond 1 nm. While the enhanced lateral diffusion coefficients persist into deeper regions of the water film than any other measure of the hydrophobic effect examined in this work, the range of influence of the surface on the dynamics of water falls dramatically short of the range for hydrophobic interactions measured in some experiments.

Theoretical study of the dynamics of F+alkanethiol self-assembled monolayer hydrogen-abstraction reactions.

The dynamics of the reactions of F atoms with octanethiol self-assembled monolayers (SAMs) has been studied using theoretical methods. F+SAM classical trajectories have been propagated directly using a quantum-mechanics (QM)/molecular-mechanics scheme in which the QM portion is described using a specific-reaction-parameters (SRP) semiempirical Hamiltonian. This SRP Hamiltonian has been derived using ab initio information of model gas-phase F+alkane reactions and its accuracy has been calibrated via comparison of the result of direct-dynamics calculations with available experiments on the F+CH(4)-->HF+CH(3) and F+C(2)H(6)-->HF+C(2)H(5) reactions. The F+SAM calculations are used to analyze HF product-energy distributions at collision energies ranging from 0.80 to 11.53 kcal mol(-1) and 0 degrees, 30 degrees, and 60 degrees incident angles with respect to the surface normal. The calculations show that while the HF product is vibrationally excited, it desorbs translationally and rotationally cold at all collision energies and incident angles explored. The calculated results shed light into recent experiments of F-atom reactions with liquid alkane surfaces by providing mechanistic understanding of the factors that govern the amount of energy deposited into the various degrees of freedom of the HF product. Specifically, examination of the dynamics of postreaction HF collisions with the surface shows the role that secondary collisions play in quenching rotational and translational excitation of HF before desorption from the surface.

Direct-dynamics study of the F + CH4, C2H6, C3H8, and i-C4H10 reactions.

We present a theoretical study of the dynamics of the first few members of the F + alkane --> HF + alkyl family of reactions (alkane = CH(4), C(2)H(6), C(3)H(8), and i-C(4)H(10)). Quasiclassical trajectories have been propagated employing a reparameterized semiempirical Hamiltonian that was derived in this work based on ab initio information of the global potential-energy surfaces of all reactions studied. The accuracy of the Hamiltonian is probed via comparison of the calculated dynamics properties with experimental results in the F + CH(4) --> HF + CH(3), F + CD(4) --> DF + CD(3), and F + C(2)H(6) --> HF + C(2)H(5) reactions. Additional calculations on the F + C(3)H(8) --> HF + C(3)H(7) and F + i-C(4)H(10) --> HF + C(4)H(9) reactions have been analyzed with emphasis on the difference in the dynamics of reactions occurring at primary, secondary, and tertiary sites. We learn that at low collision energies, the amount of energy going into HF vibration increases very slightly along the primary --> secondary --> tertiary sequence. In addition, reactions involving larger alkane molecules tend to channel more energy toward alkyl products at the expense of the rest of the degrees of freedom. Angular distributions are also dependent on the abstraction site, with tertiary abstractions resulting in slightly more backward scattering than reactions at primary sites.

Theoretical study of the dynamics of the H+CH4 and H+C2H6 reactions using a specific-reaction-parameter semiempirical Hamiltonian.

We present a theoretical study of the reactions of hydrogen atoms with methane and ethane molecules and isotopomers. High-accuracy electronic-structure calculations have been carried out to characterize representative regions of the potential-energy surface (PES) of various reaction pathways, including H abstraction and H exchange. These ab initio calculations have been subsequently employed to derive an improved set of parameters for the modified symmetrically-orthogonalized intermediate neglect of differential overlap (MSINDO) semiempirical Hamiltonian, which are specific to the H+alkane family of reactions. The specific-reaction-parameter (SRP) Hamiltonian has then been used to perform a quasiclassical-trajectory study of both the H+CH4 and H+C2H6 reactions. The calculated values of dynamics properties of the H+CH4-->H2+CH3 reaction and isotopologues, including alkyl product speed distributions, diatomic product internal-state distributions, and cross sections, are generally in good agreement with experiment and with the results provided by the ZBB3 PES [Z. Xie et al., J. Chem. Phys. 125, 133120 (2006)]. The results of trajectories propagated with the SRP Hamiltonian for the H+C2H6-->H2+C2H5 reaction also agree with experiment. The level of agreement between the results calculated with the SRP Hamiltonian and experiment in both the H+methane and H+ethane reactions indicates that semiempirical Hamiltonians can be improved for not only a specific reaction but also a family of reactions.